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- PDB-1ayl: PHOSPHOENOLPYRUVATE CARBOXYKINASE -

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Basic information

Entry
Database: PDB / ID: 1ayl
TitlePHOSPHOENOLPYRUVATE CARBOXYKINASE
ComponentsPHOSPHOENOLPYRUVATE CARBOXYKINASE
KeywordsKINASE (TRANSPHOSPHORYLATING) / P-LOOP / PROTEIN-ATP COMPLEX / NUCLEOTIDE-TRIPHOSPHATE HYDROLASE
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal ...Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / OXALATE ION / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsTari, L.W. / Pugazenthi, U. / Goldie, H. / Delbaere, L.T.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Snapshot of an enzyme reaction intermediate in the structure of the ATP-Mg2+-oxalate ternary complex of Escherichia coli PEP carboxykinase.
Authors: Tari, L.W. / Matte, A. / Pugazhenthi, U. / Goldie, H. / Delbaere, L.T.
#1: Journal: To be Published
Title: Allosteric Control by Calcium and Mechanism of Desensitization of Phosphoenolpyruvate Carboxykinase of Escherichia Coli
Authors: Goldie, H. / Sanwal, B.D.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structure of Escherichia Coli Phosphoenolpyruvate Carboxykinase: A New Structural Family with the P-Loop Nucleoside Triphosphate Hydrolase Fold
Authors: Matte, A. / Goldie, H. / Sweet, R.M. / Delbaere, L.T.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization of the Calcium-Activated Phosphoenolpyruvate Carboxykinase from Escherichia Coli K12
Authors: Delbaere, L.T. / Vandonselaar, M. / Glaeske, D. / Jabs, C. / Goldie, H.
#4: Journal: J.Bacteriol. / Year: 1990
Title: Sequence of the Pcka Gene of Escherichia Coli K-12: Relevance to Genetic and Allosteric Regulation and Homology of E. Coli Phosphoenolpyruvate Carboxykinase with the Enzymes from Trypanosoma ...Title: Sequence of the Pcka Gene of Escherichia Coli K-12: Relevance to Genetic and Allosteric Regulation and Homology of E. Coli Phosphoenolpyruvate Carboxykinase with the Enzymes from Trypanosoma Brucei and Saccharomyces Cerevisiae
Authors: Medina, V. / Pontarollo, R. / Glaeske, D. / Tabel, H. / Goldie, H.
History
DepositionDec 7, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOENOLPYRUVATE CARBOXYKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4164
Polymers59,7961
Non-polymers6203
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.510, 96.690, 46.960
Angle α, β, γ (deg.)90.00, 96.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PHOSPHOENOLPYRUVATE CARBOXYKINASE / / ATP-OXALOACETATE CARBOXY-LYASE (ATP)


Mass: 59796.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ORDERED MAGNESIUM ION OBSERVED BOUND TO ATP / Source: (natural) Escherichia coli (E. coli) / Strain: K12
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)
#2: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlPCK1drop
22 mMATP1drop
32 mMoxalate1drop
45 mM1dropMgCl2
51 mMEDTA1drop
6100 mMsodium acetate1drop
7200 mMammonium acetate1drop
812 %(w/v)PEG40001drop
9100 mMsodium acetate1reservoir
10200 mMammonium acetate1reservoir
1127 %(w/v)PEG40001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 40067 / % possible obs: 76.7 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 1.8 Å

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Processing

Software
NameClassification
X-PLORrefinement
WEISdata reduction
RefinementResolution: 1.8→6 Å / σ(F): 2
Details: MET 477 HAS DISALLOWED RAMACHANDRAN ANGLES; THE DEPOSITORS ACCOUNT FOR THIS AS IT IS THE SECOND RESIDUE WITHIN A GAMMA-TURN.
RfactorNum. reflection
Rfree0.234 -
Rwork0.195 -
obs0.195 35508
Displacement parametersBiso mean: 21.42 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 38 345 4490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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